I have seen that this bug goes for all the changed menu entries I have. I though it might be general (affecting *all* parts of the "Programs" menu, including Gnome apps), but after checking, it seems as if it just affects the Wine part of it. Changing any program in the Gnome part will bring up an error dialog when trying to execute.
To replicate this bug, just download any Win32 app, install it, make sure it runs from the menu.
Now use the menu editor and change the entry to execute whatever you want (like "yada yada"). Try it. It will still function.
As mentioned above, each CHANGED menu entry in the Wine part of the menu has two files associated with it in the ~/.local/share/applications/wine/ directory.
Unchanged entries just have one, which makes me believe the fix might be as simple as substituting "-" for "/" in a regexp somewhere.
The other reason can be that file with "-" is meant to be a form of override (for instance to be used when the menus are "global"), but alacarte doesn't take that into account when executing. Just speculations on the logic, of course.
Here's the output of find. The "Check for New Update" entry is the only one that has changes, as you can see.
.local/share/applications/wine/Programmer/FairUse Wizard 2
.local/share/applications/wine/Programmer/FairUse Wizard 2/Check for New Update.desktop
.local/share/applications/wine/Programmer/FairUse Wizard 2/FAQ.desktop
.local/share/applications/wine/Programmer/FairUse Wizard 2/License.desktop
.local/share/applications/wine/Programmer/FairUse Wizard 2/FairUse Wizard 2.desktop
.local/share/applications/wine/Programmer/FairUse Wizard 2/Uninstall FairUse Wizard 2.desktop
.local/share/applications/wine-Programmer-FairUse Wizard 2-Check for New Update.desktop